首页 > 最新文献

Open Bioinformatics Journal最新文献

英文 中文
Emergent Principles in Gene Expression Dynamics 基因表达动力学中的涌现原理
Q3 Computer Science Pub Date : 2011-02-02 DOI: 10.2174/1875036201105010034
J. Nacher, T. Ochiai
Rapid advances in data processing of genome-wide gene expression have allowed us to get a first glimpse of some fundamental laws and principles involved in the intra-cellular organization as well as to investigate its complex regulatory architecture. However, the identification of commonalities in dynamical processes involved in networks has not followed the same development. In particular, the coupling between dynamics and structural features remains largely uncovered. Here, we review several works that have addressed the issue of uncovering the gene expression dynamics and principles using micro-array time series data at different environmental conditions and disease states as well as the emer- gence of criticality in gene expression systems by using information theory. Moreover, we also describe the efforts done to explore the question of characterizing gene networks by using transcriptional dynamics information. The combination of the emergent principles uncovered in the transcriptional organization with dynamic information, may lead to recon- struct, characterize and complete gene networks. We also discuss several methods based on simulations of a series of en- zyme-catalyzed reaction routes and Markov processes as well as combination of complex network properties with sto- chastic theory.
全基因组基因表达数据处理的快速发展使我们能够初步了解细胞内组织的一些基本规律和原理,并研究其复杂的调控结构。然而,识别网络中涉及的动态过程的共性并没有遵循相同的发展。特别是,动力学和结构特征之间的耦合在很大程度上仍未发现。在这里,我们回顾了几项研究,这些研究利用微阵列时间序列数据揭示了不同环境条件和疾病状态下基因表达的动态和原理,以及利用信息论揭示了基因表达系统中临界性的出现。此外,我们还描述了通过使用转录动力学信息来探索表征基因网络的问题所做的努力。将转录组织中揭示的涌现原理与动态信息相结合,可能导致基因网络的重构、表征和完整。我们还讨论了几种基于一系列酶催化反应路线和马尔可夫过程的模拟方法,以及将复杂网络性质与随机理论相结合的方法。
{"title":"Emergent Principles in Gene Expression Dynamics","authors":"J. Nacher, T. Ochiai","doi":"10.2174/1875036201105010034","DOIUrl":"https://doi.org/10.2174/1875036201105010034","url":null,"abstract":"Rapid advances in data processing of genome-wide gene expression have allowed us to get a first glimpse of some fundamental laws and principles involved in the intra-cellular organization as well as to investigate its complex regulatory architecture. However, the identification of commonalities in dynamical processes involved in networks has not followed the same development. In particular, the coupling between dynamics and structural features remains largely uncovered. Here, we review several works that have addressed the issue of uncovering the gene expression dynamics and principles using micro-array time series data at different environmental conditions and disease states as well as the emer- gence of criticality in gene expression systems by using information theory. Moreover, we also describe the efforts done to explore the question of characterizing gene networks by using transcriptional dynamics information. The combination of the emergent principles uncovered in the transcriptional organization with dynamic information, may lead to recon- struct, characterize and complete gene networks. We also discuss several methods based on simulations of a series of en- zyme-catalyzed reaction routes and Markov processes as well as combination of complex network properties with sto- chastic theory.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106211","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Stability and Flexibility from a System Analysis of Gene Regulatory Networks Based on Ordinary Differential Equations 基于常微分方程的基因调控网络系统分析的稳定性和灵活性
Q3 Computer Science Pub Date : 2011-02-02 DOI: 10.2174/1875036201105010026
M. Gustafsson, Michael Hörnquist
The inference of large-scale gene regulatory networks from high-throughput data sets has revealed a diverse picture of only partially overlapping descriptions. Nevertheless, several properties in t ...
从高通量数据集推断出的大规模基因调控网络揭示了只有部分重叠描述的多样化图景。然而,t中的几个属性…
{"title":"Stability and Flexibility from a System Analysis of Gene Regulatory Networks Based on Ordinary Differential Equations","authors":"M. Gustafsson, Michael Hörnquist","doi":"10.2174/1875036201105010026","DOIUrl":"https://doi.org/10.2174/1875036201105010026","url":null,"abstract":"The inference of large-scale gene regulatory networks from high-throughput data sets has revealed a diverse picture of only partially overlapping descriptions. Nevertheless, several properties in t ...","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106727","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Topological determinants of synchronizability of oscillators on large complex networks 大型复杂网络上振子同步性的拓扑决定因素
Q3 Computer Science Pub Date : 2011-02-02 DOI: 10.2174/1875036201105010042
Weihan Li, Changsong Zhou
Synchronized oscillations play an important role in many biological systems. In recent years, much work has been done on oscillating biomolecular systems, both experimentally and theoretically. A better insight into oscillation mechanisms, coupling strategies and related biological processes is gained by quantitative analysis. Here we summarized some of recent work on oscillation and synchronization in biological systems and reviewed the basic concepts of synchronization of coupled oscillators and dynamics on complex networks.
同步振荡在许多生物系统中起着重要作用。近年来,人们对振荡生物分子系统进行了大量的实验和理论研究。通过定量分析可以更好地了解振荡机制、耦合策略和相关的生物过程。本文综述了近年来生物系统中振荡与同步的研究进展,并对耦合振荡同步和复杂网络动力学的基本概念进行了综述。
{"title":"Topological determinants of synchronizability of oscillators on large complex networks","authors":"Weihan Li, Changsong Zhou","doi":"10.2174/1875036201105010042","DOIUrl":"https://doi.org/10.2174/1875036201105010042","url":null,"abstract":"Synchronized oscillations play an important role in many biological systems. In recent years, much work has been done on oscillating biomolecular systems, both experimentally and theoretically. A better insight into oscillation mechanisms, coupling strategies and related biological processes is gained by quantitative analysis. Here we summarized some of recent work on oscillation and synchronization in biological systems and reviewed the basic concepts of synchronization of coupled oscillators and dynamics on complex networks.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Boolean modeling of biochemical networks 生化网络的布尔建模
Q3 Computer Science Pub Date : 2011-02-02 DOI: 10.2174/1875036201105010016
T. Helikar, Naomi Kochi, J. Konvalina, J. Rogers
The use of modeling to observe and analyze the mechanisms of complex biochemical network function is be- coming an important methodological tool in the systems biology era. Number of different approaches to model these net- works have been utilized-- they range from analysis of static connection graphs to dynamical models based on kinetic in- teraction data. Dynamical models have a distinct appeal in that they make it possible to observe these networks in action, but they also pose a distinct challenge in that they require detailed information describing how the individual components of these networks interact in living cells. Because this level of detail is generally not known, dynamic modeling requires simplifying assumptions in order to make it practical. In this review Boolean modeling will be discussed, a modeling method that depends on the simplifying assumption that all elements of a network exist only in one of two states.
利用建模来观察和分析复杂生化网络功能的机制是系统生物学时代重要的方法论工具。已经使用了许多不同的方法来对这些网络进行建模——它们的范围从静态连接图的分析到基于动态交互数据的动态模型。动态模型具有独特的吸引力,因为它们使观察这些网络的作用成为可能,但它们也提出了一个独特的挑战,因为它们需要详细的信息来描述这些网络的各个组成部分如何在活细胞中相互作用。由于这种级别的细节通常不为人所知,动态建模需要简化假设以使其实用。本文将讨论布尔建模,这是一种基于简化假设的建模方法,即网络的所有元素只存在于两种状态中的一种。
{"title":"Boolean modeling of biochemical networks","authors":"T. Helikar, Naomi Kochi, J. Konvalina, J. Rogers","doi":"10.2174/1875036201105010016","DOIUrl":"https://doi.org/10.2174/1875036201105010016","url":null,"abstract":"The use of modeling to observe and analyze the mechanisms of complex biochemical network function is be- coming an important methodological tool in the systems biology era. Number of different approaches to model these net- works have been utilized-- they range from analysis of static connection graphs to dynamical models based on kinetic in- teraction data. Dynamical models have a distinct appeal in that they make it possible to observe these networks in action, but they also pose a distinct challenge in that they require detailed information describing how the individual components of these networks interact in living cells. Because this level of detail is generally not known, dynamic modeling requires simplifying assumptions in order to make it practical. In this review Boolean modeling will be discussed, a modeling method that depends on the simplifying assumption that all elements of a network exist only in one of two states.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 42
Exploring the Dynamics of Large-Scale Biochemical Networks: A Computational Perspective 探索大规模生化网络的动力学:一个计算的视角
Q3 Computer Science Pub Date : 2011-02-02 DOI: 10.2174/1875036201105010004
R. Steuer
The complexity of even comparatively simple biochemical systems necessitates a computational description to explore and eventually understand the dynamics emerging from the underlying networks of cellular interactions. Within this contribution, several aspects relating to a computational description of large-scale biochemical networks are discussed. Topics range from a brief description of the rationales for computational modeling to the utilization of Monte Carlo methods to explore dynamic properties of biochemical networks. The main focus is to outline a path towards the construction of large-scale kinetic models of metabolic networks in the face of incomplete and uncertain knowledge of kinetic parameters. It is argued that a combination of phenotypic data, large-scale measurements, heuristic assumptions about generic rate equations, together with appropriate numerical schemes, allows for a fast and efficient way to explore the dynamic properties of biochemical networks. In this respect, several recently proposed strategies that are based on Monte Carlo methods are an important step towards large-scale kinetic models of cellular metabolism.
即使是相对简单的生化系统的复杂性,也需要一个计算描述来探索并最终理解从细胞相互作用的潜在网络中出现的动态。在这个贡献中,讨论了与大规模生化网络的计算描述有关的几个方面。主题范围从计算建模的基本原理的简要描述到利用蒙特卡罗方法来探索生化网络的动态特性。主要重点是在面对不完整和不确定的动力学参数知识的情况下,勾勒出一条通往构建大规模代谢网络动力学模型的路径。本文认为,结合表型数据、大规模测量、关于一般速率方程的启发式假设以及适当的数值方案,可以快速有效地探索生化网络的动态特性。在这方面,最近提出的几种基于蒙特卡罗方法的策略是迈向大规模细胞代谢动力学模型的重要一步。
{"title":"Exploring the Dynamics of Large-Scale Biochemical Networks: A Computational Perspective","authors":"R. Steuer","doi":"10.2174/1875036201105010004","DOIUrl":"https://doi.org/10.2174/1875036201105010004","url":null,"abstract":"The complexity of even comparatively simple biochemical systems necessitates a computational description to explore and eventually understand the dynamics emerging from the underlying networks of cellular interactions. Within this contribution, several aspects relating to a computational description of large-scale biochemical networks are discussed. Topics range from a brief description of the rationales for computational modeling to the utilization of Monte Carlo methods to explore dynamic properties of biochemical networks. The main focus is to outline a path towards the construction of large-scale kinetic models of metabolic networks in the face of incomplete and uncertain knowledge of kinetic parameters. It is argued that a combination of phenotypic data, large-scale measurements, heuristic assumptions about generic rate equations, together with appropriate numerical schemes, allows for a fast and efficient way to explore the dynamic properties of biochemical networks. In this respect, several recently proposed strategies that are based on Monte Carlo methods are an important step towards large-scale kinetic models of cellular metabolism.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 9
Editorial: Structure, Dynamics and Function - Dynamical Properties of Large Bio-Molecular Networks 编辑:结构、动力学与功能——大型生物分子网络的动力学特性
Q3 Computer Science Pub Date : 2011-02-02 DOI: 10.2174/1875036201104010001
A. Fuente
Bio-molecular systems consist of tens of thousands of molecular species of different chemical nature. These systems have been described as networks, such as metabolic networks [1, 2], protein-interaction networks [3], and transcriptional regulatory networks [4]. The nodes in these networks represent bio-molecular species (e.g. metabolites, proteins, RNAs) and the edges represent functional, causal or physical interactions between the nodes. The abstract representation of bio-molecular regulatory systems as networks is fruitful because it provides the ability to study the systems as a whole while ignoring many irrelevant details [5, 6]. All chemistry and physics is removed (or considered only implicitly) in order to concentrate on the essence of the system: the 'wiring scheme'. As for all abstractions of natural systems, we are doomed to lose some information when we represent bio-molecular regulatory systems as networks [6-8]. Large bio-molecular network have been subjected extensively to topological analysis for over a decade now. Many interesting topological features have been identified and their potential functions have been proposed [5, 6]. However, relating the structure of large bio-molecular network to dynamics and function is still a largely unexplored subject. Studies on dynamical properties have mostly been restricted to very small bio-molecular networks, due to the limited amount of quantitative data. Fortunately, several studies have shown that even without detailed quantitative knowledge, much can still be learned about the dynamical properties of large bio-molecular networks [9-13]. This special issue provides a recent update of the current state of art in relating structure to dynamics applied to large bio-molecular networks. The goal of the studies reviewed in this special issue is not to study the dynamics of any specific bio-molecular network, but rather to identify topological patterns which imply the possibility of certain dynamical/functional behaviors. By no means can we definitely state that 'structure determines function' as networks with the same structure could display distinct dynamics depending on their parameter values (for instance the strength or signs of interactions). Networks could for instance display oscillations or reach a stable steady state depending on the specific model parameters. To be able to characterize the true behavior of bio-molecular networks we need the quantitative information of all the parameters. Experimental identification of the large numbers of parameters is currently infeasible, even with modern high throughput techniques. Nevertheless, we can still learn much about dynamics from topology alone. Inspection of the network topology can immediately exclude certain dynamical behaviors completely …
生物分子系统由数以万计的具有不同化学性质的分子种类组成。这些系统被描述为网络,如代谢网络[1,2]、蛋白质相互作用网络[3]和转录调节网络[4]。这些网络中的节点代表生物分子物种(如代谢物、蛋白质、rna),边缘代表节点之间的功能、因果或物理相互作用。将生物分子调控系统抽象表示为网络是富有成效的,因为它提供了将系统作为一个整体来研究的能力,同时忽略了许多不相关的细节[5,6]。为了专注于系统的本质:“布线方案”,所有的化学和物理都被移除了(或只是含蓄地考虑)。对于所有自然系统的抽象,当我们将生物分子调控系统表示为网络时,注定会丢失一些信息[6-8]。十多年来,人们对大型生物分子网络进行了广泛的拓扑分析。已经发现了许多有趣的拓扑特征,并提出了它们的潜在函数[5,6]。然而,将大型生物分子网络的结构与动力学和功能联系起来仍然是一个很大程度上未被探索的课题。由于定量数据有限,对动力学性质的研究大多局限于非常小的生物分子网络。幸运的是,一些研究表明,即使没有详细的定量知识,仍然可以了解大型生物分子网络的动力学特性[9-13]。本期特刊提供了应用于大型生物分子网络的有关结构与动力学的最新进展。本特刊回顾的研究目标不是研究任何特定生物分子网络的动力学,而是确定暗示某些动力学/功能行为可能性的拓扑模式。我们绝对不能说“结构决定功能”,因为具有相同结构的网络可以根据其参数值(例如相互作用的强度或迹象)显示不同的动态。例如,网络可以根据特定的模型参数显示振荡或达到稳定的稳定状态。为了能够描述生物分子网络的真实行为,我们需要所有参数的定量信息。即使使用现代高通量技术,对大量参数进行实验鉴定目前也是不可行的。尽管如此,我们仍然可以从拓扑学中学到很多动力学知识。检查网络拓扑结构可以立即排除某些动态行为完全…
{"title":"Editorial: Structure, Dynamics and Function - Dynamical Properties of Large Bio-Molecular Networks","authors":"A. Fuente","doi":"10.2174/1875036201104010001","DOIUrl":"https://doi.org/10.2174/1875036201104010001","url":null,"abstract":"Bio-molecular systems consist of tens of thousands of molecular species of different chemical nature. These systems have been described as networks, such as metabolic networks [1, 2], protein-interaction networks [3], and transcriptional regulatory networks [4]. The nodes in these networks represent bio-molecular species (e.g. metabolites, proteins, RNAs) and the edges represent functional, causal or physical interactions between the nodes. The abstract representation of bio-molecular regulatory systems as networks is fruitful because it provides the ability to study the systems as a whole while ignoring many irrelevant details [5, 6]. All chemistry and physics is removed (or considered only implicitly) in order to concentrate on the essence of the system: the 'wiring scheme'. As for all abstractions of natural systems, we are doomed to lose some information when we represent bio-molecular regulatory systems as networks [6-8]. Large bio-molecular network have been subjected extensively to topological analysis for over a decade now. Many interesting topological features have been identified and their potential functions have been proposed [5, 6]. However, relating the structure of large bio-molecular network to dynamics and function is still a largely unexplored subject. Studies on dynamical properties have mostly been restricted to very small bio-molecular networks, due to the limited amount of quantitative data. Fortunately, several studies have shown that even without detailed quantitative knowledge, much can still be learned about the dynamical properties of large bio-molecular networks [9-13]. This special issue provides a recent update of the current state of art in relating structure to dynamics applied to large bio-molecular networks. The goal of the studies reviewed in this special issue is not to study the dynamics of any specific bio-molecular network, but rather to identify topological patterns which imply the possibility of certain dynamical/functional behaviors. By no means can we definitely state that 'structure determines function' as networks with the same structure could display distinct dynamics depending on their parameter values (for instance the strength or signs of interactions). Networks could for instance display oscillations or reach a stable steady state depending on the specific model parameters. To be able to characterize the true behavior of bio-molecular networks we need the quantitative information of all the parameters. Experimental identification of the large numbers of parameters is currently infeasible, even with modern high throughput techniques. Nevertheless, we can still learn much about dynamics from topology alone. Inspection of the network topology can immediately exclude certain dynamical behaviors completely …","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Protein Kinase-Regulated Inwardly Rectifying Anion and Organic Osmolyte Channels in Malaria-Infected Erythrocytes 疟疾感染红细胞中蛋白激酶调节的内校正阴离子和有机渗透通道
Q3 Computer Science Pub Date : 2011-01-31 DOI: 10.2174/1874196701104010010
G. Bouyer, Serge L. Y. Thomas, S. Egée
The intraerythrocytic amplification of the malaria parasite Plasmodium falciparum induces new pathways of solute permeability in the host cell's membrane. These pathways play a pivotal role in parasite development by supplying the parasite with nutrients, disposing of the parasite's metabolic waste and organic osmolytes, and adapting the host's electrolyte composition to the parasite's needs. During the last ten years, electrophysiological investigations strongly supported earlier evidence obtained by transport and pharmacological studies that this new permeability pathway, which is induced by the parasite in the host cell membrane, is constituted by anion-selective channels. This review surveys the evidences acquired using the patch-clamp technique and discuss the hypothesis that protein kinase A is an effector of the signalling pathway leading to the activation of endogenous channels upon infection.
疟原虫恶性疟原虫的红细胞内扩增诱导宿主细胞膜溶质渗透的新途径。这些途径在寄生虫的发育过程中发挥着关键作用,为寄生虫提供营养,处理寄生虫的代谢废物和有机渗透物,并使宿主的电解质组成适应寄生虫的需要。近十年来,电生理研究有力地支持了早期转运和药理学研究的证据,即寄生虫在宿主细胞膜上诱导的这种新的渗透性途径是由阴离子选择通道构成的。本文综述了利用膜片钳技术获得的证据,并讨论了蛋白激酶A是导致内源性通道在感染时激活的信号通路的效应者的假设。
{"title":"Protein Kinase-Regulated Inwardly Rectifying Anion and Organic Osmolyte Channels in Malaria-Infected Erythrocytes","authors":"G. Bouyer, Serge L. Y. Thomas, S. Egée","doi":"10.2174/1874196701104010010","DOIUrl":"https://doi.org/10.2174/1874196701104010010","url":null,"abstract":"The intraerythrocytic amplification of the malaria parasite Plasmodium falciparum induces new pathways of solute permeability in the host cell's membrane. These pathways play a pivotal role in parasite development by supplying the parasite with nutrients, disposing of the parasite's metabolic waste and organic osmolytes, and adapting the host's electrolyte composition to the parasite's needs. During the last ten years, electrophysiological investigations strongly supported earlier evidence obtained by transport and pharmacological studies that this new permeability pathway, which is induced by the parasite in the host cell membrane, is constituted by anion-selective channels. This review surveys the evidences acquired using the patch-clamp technique and discuss the hypothesis that protein kinase A is an effector of the signalling pathway leading to the activation of endogenous channels upon infection.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68052932","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
The Outward Rectifying Anions and Organic Osmolytes Conductance in Malaria-Infected Erythocytes: Myth or Reality? 疟疾感染红细胞的外正性阴离子和有机渗透细胞电导率:神话还是现实?
Q3 Computer Science Pub Date : 2011-01-31 DOI: 10.2174/1874196701104010003
C. Duranton, Tanneur Valerie, Tauc Michel
Malaria-infected erythrocytes acquired New Permeability Pathways (NPPs) to meet the needs in nutrients and disposal of waste products of the intraerythocytic parasite development. The NPPs have been intensively studied for their putative interest as therapeutic targets for malaria treatment. Over the past 10 years, many electrophysiological studies have identified novel ion conductances (reflecting a part of the NPPs activities) in the host plasma membrane of Plasmodium falciparum-infected erythrocytes. In this article, we review the electrophysiological/biophysical properties of the malaria-induced outwardly rectifying anion conductance and compare this conductance to the other anion conductances and permeabilities already described in the literature.
疟疾感染的红细胞获得了新的渗透性通路(NPPs),以满足红细胞内寄生虫发育对营养和废物处理的需要。人们对npp进行了深入研究,因为它们被认为有兴趣作为疟疾治疗的治疗靶点。在过去的10年里,许多电生理研究已经发现了恶性疟原虫感染红细胞的宿主质膜中新的离子电导(反映了部分NPPs活性)。在本文中,我们回顾了疟疾诱导的向外整流阴离子电导率的电生理/生物物理特性,并将其与文献中描述的其他阴离子电导率和渗透性进行了比较。
{"title":"The Outward Rectifying Anions and Organic Osmolytes Conductance in Malaria-Infected Erythocytes: Myth or Reality?","authors":"C. Duranton, Tanneur Valerie, Tauc Michel","doi":"10.2174/1874196701104010003","DOIUrl":"https://doi.org/10.2174/1874196701104010003","url":null,"abstract":"Malaria-infected erythrocytes acquired New Permeability Pathways (NPPs) to meet the needs in nutrients and disposal of waste products of the intraerythocytic parasite development. The NPPs have been intensively studied for their putative interest as therapeutic targets for malaria treatment. Over the past 10 years, many electrophysiological studies have identified novel ion conductances (reflecting a part of the NPPs activities) in the host plasma membrane of Plasmodium falciparum-infected erythrocytes. In this article, we review the electrophysiological/biophysical properties of the malaria-induced outwardly rectifying anion conductance and compare this conductance to the other anion conductances and permeabilities already described in the literature.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68052918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ClC-2 Channels in Erythrocytes 红细胞中的ClC-2通道
Q3 Computer Science Pub Date : 2011-01-31 DOI: 10.2174/1874196701104010018
E. Shumilina, S. Huber
ClC-2 is a ubiquitously expressed plasma membrane Cl - channel that reportedly controls the ionic environment in mouse retina and testis. Beyond that, ClC-2 might sense cellular energy status and cellular stress by its carboxy- terminal cystathionine-beta-synthase (CBS) domains and by its molecular interaction with the heat shock protein Hsp90, respectively. In mature human and mouse erythrocytes, ClC-2 is activated by oxidative stress and by malaria infection. This article describes possible function of erythrocyte ClC-2 channels for the programmed death of oxidatively injured erythrocytes and for the regulatory volume decrease of malaria-infected erythrocytes.
ClC-2是一种普遍表达的质膜Cl -通道,据报道,它控制着小鼠视网膜和睾丸的离子环境。除此之外,ClC-2可能分别通过其羧基端胱硫氨酸- β合成酶(CBS)结构域和与热休克蛋白Hsp90的分子相互作用来感知细胞能量状态和细胞应激。在成熟的人和小鼠红细胞中,ClC-2可被氧化应激和疟疾感染激活。本文描述了红细胞ClC-2通道在氧化损伤红细胞程序性死亡和疟疾感染红细胞调节性体积减少中的可能功能。
{"title":"ClC-2 Channels in Erythrocytes","authors":"E. Shumilina, S. Huber","doi":"10.2174/1874196701104010018","DOIUrl":"https://doi.org/10.2174/1874196701104010018","url":null,"abstract":"ClC-2 is a ubiquitously expressed plasma membrane Cl - channel that reportedly controls the ionic environment in mouse retina and testis. Beyond that, ClC-2 might sense cellular energy status and cellular stress by its carboxy- terminal cystathionine-beta-synthase (CBS) domains and by its molecular interaction with the heat shock protein Hsp90, respectively. In mature human and mouse erythrocytes, ClC-2 is activated by oxidative stress and by malaria infection. This article describes possible function of erythrocyte ClC-2 channels for the programmed death of oxidatively injured erythrocytes and for the regulatory volume decrease of malaria-infected erythrocytes.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68052942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Editorial: Ion Channels of Mature Human Erythrocytes 社论:成熟人红细胞的离子通道
Q3 Computer Science Pub Date : 2011-01-31 DOI: 10.2174/18750362010040100001
H. Stephan
Ion channels in the plasma membrane serve multiple functions such as setting the membrane potential, adjusting the cell volume and the intracellular electrolyte concentrations or eliciting versatile cytosolic Ca signals. Channel activities regulate many basic cellular processes. Among those are cell proliferation, migration, differentiation and apoptotic cell death. Although devoid of nuclei and mitochondria, mature mammalian erythrocytes maintain a full set of functional ion channels in their plasma membrane.
质膜上的离子通道具有多种功能,如设置膜电位,调节细胞体积和细胞内电解质浓度或激发多种胞质钙信号。通道活动调节许多基本的细胞过程。其中包括细胞增殖、迁移、分化和细胞凋亡。尽管缺乏细胞核和线粒体,成熟的哺乳动物红细胞在其质膜上保持着一整套功能的离子通道。
{"title":"Editorial: Ion Channels of Mature Human Erythrocytes","authors":"H. Stephan","doi":"10.2174/18750362010040100001","DOIUrl":"https://doi.org/10.2174/18750362010040100001","url":null,"abstract":"Ion channels in the plasma membrane serve multiple functions such as setting the membrane potential, adjusting the cell volume and the intracellular electrolyte concentrations or eliciting versatile cytosolic Ca signals. Channel activities regulate many basic cellular processes. Among those are cell proliferation, migration, differentiation and apoptotic cell death. Although devoid of nuclei and mitochondria, mature mammalian erythrocytes maintain a full set of functional ion channels in their plasma membrane.","PeriodicalId":38956,"journal":{"name":"Open Bioinformatics Journal","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2011-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68106349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
期刊
Open Bioinformatics Journal
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1